From 1703717285d90b4a1f4d55552df8f35eac0a7418 Mon Sep 17 00:00:00 2001 From: "James E. Housley" Date: Tue, 10 Oct 2000 11:14:03 +0000 Subject: Initial import of biology/biojava PR: 21678 Submitted by: Brad Chapman --- biology/biojava/Makefile | 59 +++++ biology/biojava/distinfo | 1 + biology/biojava/pkg-comment | 1 + biology/biojava/pkg-descr | 11 + biology/biojava/pkg-plist | 588 ++++++++++++++++++++++++++++++++++++++++++++ 5 files changed, 660 insertions(+) create mode 100644 biology/biojava/Makefile create mode 100644 biology/biojava/distinfo create mode 100644 biology/biojava/pkg-comment create mode 100644 biology/biojava/pkg-descr create mode 100644 biology/biojava/pkg-plist (limited to 'biology/biojava') diff --git a/biology/biojava/Makefile b/biology/biojava/Makefile new file mode 100644 index 000000000000..76fe2ff54f1e --- /dev/null +++ b/biology/biojava/Makefile @@ -0,0 +1,59 @@ +# New ports collection makefile for: biojava +# Date created: 15 September 2000 +# Whom: FreeBSD Bio porters (bio@freebsd.net) +# +# $FreeBSD$ +# + +PORTNAME= biojava +PORTVERSION= 1.01 +CATEGORIES= biology java +MASTER_SITES= ftp://ftp.biojava.org/pub/biojava/source/ + +MAINTAINER= bio@freebsd.net + +BUILD_DEPENDS= ${JAVA_COMMAND}:${PORTSDIR}/java/linux-jdk + +JDK_VERSION= 1.2.2 +JAVAVERSION= linux-jdk${JDK_VERSION} +JAVADIR= ${PREFIX}/${JAVAVERSION} +JAVA_COMPILE= ${JAVADIR}/bin/javac +JAVA_COMMAND= ${JAVADIR}/bin/java + +do-build: + @(cd ${WRKSRC}; \ + ${JAVA_COMPILE} build/Builder.java; \ + ${SETENV} PATH=${PATH}:${JAVADIR}/bin \ + ${JAVA_COMMAND} build.Builder all;) + +.if !defined(NOPORTDOCS) + @(cd ${WRKSRC}; ${SETENV} PATH=${PATH}:${JAVADIR}/bin \ + ${JAVA_COMMAND} build.Builder docs;) +.endif + +do-install: + @(cd ${WRKSRC}; \ + ${MKDIR} ${PREFIX}/share/java/classes/; \ + ${CP} ${WRKSRC}/biojava.jar ${PREFIX}/share/java/classes/; \ + ${CP} ${WRKSRC}/xml.jar ${PREFIX}/share/java/classes/; \ + ${MKDIR} ${PREFIX}/share/java/${PKGNAME}/; \ + ${CP} -R README LICENSE ${PREFIX}/share/java/${PKGNAME}/; \ + ${CP} -R ${WRKSRC}/demos ${PREFIX}/share/java/${PKGNAME}/;) + +.if !defined(NOPORTDOCS) + @(${CP} -R ${WRKSRC}/docs ${PREFIX}/share/java/${PKGNAME}) +.endif) + +post-install: +.if !defined(BATCH) + @${ECHO_MSG} "" + @${ECHO_MSG} "Libraries installed at: ${PREFIX}/share/java/classes/" + @${ECHO_MSG} "You should edit your CLASSPATH to include the jar files" + @${ECHO_MSG} "in this directory." + @${ECHO_MSG} "" + @${ECHO_MSG} "Docs and demos are installed in:" + @${ECHO_MSG} "${PREFIX}/share/java/${PKGNAME}" + @${ECHO_MSG} "" +.endif + +.include diff --git a/biology/biojava/distinfo b/biology/biojava/distinfo new file mode 100644 index 000000000000..12cfd5369ece --- /dev/null +++ b/biology/biojava/distinfo @@ -0,0 +1 @@ +MD5 (biojava-1.01.tar.gz) = c4f3e397ff5f5f3b71da6c3e7b68b9b9 diff --git a/biology/biojava/pkg-comment b/biology/biojava/pkg-comment new file mode 100644 index 000000000000..bb2f70c7749d --- /dev/null +++ b/biology/biojava/pkg-comment @@ -0,0 +1 @@ +Open-source java tools for processing biological data diff --git a/biology/biojava/pkg-descr b/biology/biojava/pkg-descr new file mode 100644 index 000000000000..6f23cb08e8c1 --- /dev/null +++ b/biology/biojava/pkg-descr @@ -0,0 +1,11 @@ +The BioJava Project is an open-source project dedicated to providing Java +tools for processing biological data. This will include objects for +manipulating sequences, file parsers, CORBA interoperability, access to +ACeDB, dynamic programming, and simple statistical routines. + +The BioJava library is useful for automating those daily and mundane +bioinformatics tasks. As the library matures, the BioJava libraries will +provide a foundation upon which both free software and commercial packages +can be developed. + +WWW: http://www.biojava.org diff --git a/biology/biojava/pkg-plist b/biology/biojava/pkg-plist new file mode 100644 index 000000000000..c0c4de8b8630 --- /dev/null +++ b/biology/biojava/pkg-plist @@ -0,0 +1,588 @@ +share/java/classes/biojava.jar +share/java/classes/xml.jar +share/java/biojava-1.01/LICENSE +share/java/biojava-1.01/README +share/java/biojava-1.01/demos/acedb/AceTreeView.java +share/java/biojava-1.01/demos/acedb/ServeAceAsCorba.java +share/java/biojava-1.01/demos/acedb/AceClient.java +share/java/biojava-1.01/demos/acedb/SequenceFetch.java +share/java/biojava-1.01/demos/gff/GFFFilter.java +share/java/biojava-1.01/demos/gff/EmblToGffFasta.java +share/java/biojava-1.01/demos/gff/GFFToFeatures.java +share/java/biojava-1.01/demos/gff/varC4-2.gff +share/java/biojava-1.01/demos/gff/AL121903.embl 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